Research workbench
Crystal structure of the CDC25B phosphatase catalytic domain with the active site cysteine in the sulfinic form
Analyse Crystal structure of the CDC25B phosphatase catalytic domain with the active… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YM9
- Type
- protein
- Length
- 171 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- M-phase inducer phosphatase 2
- EC
- 3.1.3.48
- UniProt
- P30305
- Ligands
- CL
- Pockets
- 2 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | M-phase inducer phosphatase 2 (EC 3.1.3.48) | protein | 171 | 33% helix, 18% strand | P30305 |
Ligands and binding sites
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 71 | 0.51 | 0.85 | 16 | CL |
| 2 | 80 | 0.39 | 0.78 | 14 | empty |
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 1YM9 · Crystal structure of the CDC25B phosphatase catalytic domain with the active site… · the same entry in another collection · chain A against A, TM-score 1.00
- P30305 · AlphaFold monomer V2.0 prediction for M-phase inducer phosphatase 2 (P30305) · a predicted model of the same protein · chain A against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P30305
- Elsewhere: RCSB PDB 1YM9 · PDBe 1YM9 · UniProt P30305
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